From 1ef53c6e1e8f030bce0933c2154a7af3773b496a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 21 Jul 2006 08:48:00 +0000
Subject: [PATCH] show hide stuff moved from columnSelection

---
 src/jalview/gui/AlignViewport.java   |   56 +++++++++++++++++++++++++++++++---
 src/jalview/gui/ColumnSelection.java |   17 ++++++-----
 2 files changed, 61 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2e1a4e0..a101fcf 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -74,6 +74,7 @@ public class AlignViewport
     boolean scaleRightWrapped = true;
     boolean hasHiddenColumns = false;
     boolean hasHiddenRows = false;
+    boolean showHiddenMarkers = true;
 
     boolean cursorMode = false;
 
@@ -1119,10 +1120,44 @@ public class AlignViewport
       return isDataset;
     }
 
+
+    public void hideSelectedColumns()
+    {
+      if (colSel.selected.size() < 1)
+        return;
+
+      while (colSel.selected.size() > 0)
+      {
+        int column = ( (Integer) colSel.selected.firstElement()).intValue();
+        colSel.hideColumns(column);
+      }
+      setSelectionGroup(null);
+      hasHiddenColumns = true;
+    }
+
+
+    public void hideColumns(int start, int end)
+    {
+      if(start==end)
+        end++;
+
+      for(int i=start; i<end; i++)
+      {
+        colSel.addElement(i);
+        colSel.hideColumns(i);
+      }
+
+      setSelectionGroup(null);
+      hasHiddenColumns = true;
+    }
+
     public void hideSequence(SequenceI seq)
     {
-      alignment.getHiddenSequences().hideSequence(seq);
-      hasHiddenRows = true;
+      if(seq!=null)
+      {
+        alignment.getHiddenSequences().hideSequence(seq);
+        hasHiddenRows = true;
+      }
     }
 
     public void showSequence(int index)
@@ -1135,8 +1170,11 @@ public class AlignViewport
 
     public void showAllHiddenSeqs()
     {
-      alignment.getHiddenSequences().showAll();
-      hasHiddenRows = false;
+      if(alignment.getHiddenSequences().getSize()>0)
+      {
+        alignment.getHiddenSequences().showAll();
+        hasHiddenRows = false;
+      }
     }
 
     public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1245,4 +1283,14 @@ public class AlignViewport
 
       return selection;
     }
+
+    public boolean getShowHiddenMarkers()
+    {
+      return showHiddenMarkers;
+    }
+
+    public void setShowHiddenMarkers(boolean show)
+    {
+      showHiddenMarkers = show;
+    }
 }
diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index eb6cafe..94e2642 100755
--- a/src/jalview/gui/ColumnSelection.java
+++ b/src/jalview/gui/ColumnSelection.java
@@ -330,7 +330,8 @@ public class ColumnSelection
     }
 
 
-    public void hideColumns(int res, AlignViewport av)
+
+    public void hideColumns(int res)
     {
       if(hiddenColumns==null)
         hiddenColumns = new Vector();
@@ -360,19 +361,19 @@ public class ColumnSelection
       if(!added)
         hiddenColumns.addElement(new int[]{min, max});
 
-
-      av.setSelectionGroup(null);
-      av.hasHiddenColumns = true;
     }
 
     public void revealAllHiddenColumns(AlignViewport av)
     {
-      for(int i=0; i<hiddenColumns.size(); i++)
+      if(hiddenColumns!=null)
       {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        for(int j=region[0]; j<region[1]; j++)
+        for (int i = 0; i < hiddenColumns.size(); i++)
         {
-          addElement(j);
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          for (int j = region[0]; j < region[1]; j++)
+          {
+            addElement(j);
+          }
         }
       }
       av.hasHiddenColumns = false;
-- 
1.7.10.2